151
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Chatgilialoglu C, Caminal C, Altieri A, Vougioukalakis GC, Mulazzani QG, Gimisis T, Guerra M. Tautomerism in the guanyl radical. J Am Chem Soc 2007; 128:13796-805. [PMID: 17044708 DOI: 10.1021/ja062636h] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite a few decades of intense study, a full description of tautomers of one-electron-oxidized guanine remains to be achieved. Here we show that two of these tautomers are produced by the protonation of an 8-haloguanine electron adduct. The rate constants for the reactions of hydrated electrons (e(aq)(-)) with a variety of 8-substituted guanine derivatives have been measured by a pulse radiolysis technique and correlated with both inductive and resonance components of the substituents. The fate of electron adducts was investigated by radiolytic methods coupled with product studies and addressed computationally by means of time-dependent DFT (TD-B3LYP/6-311G**//B1B95/6-31+G**) calculations. The reaction of e(aq)(-) with 8-haloguanosine or 8-halo-2'-deoxyguanosine produces the first observable transient species that decay unimolecularly (k = 1 x 10(5) s(-)(1) at 22 degrees C) to give the one-electron oxidized guanosine or 2'-deoxyguanosine. Theory suggests that the electron adducts of 8-bromoguanine derivatives protonated at C8 form a pi-complex, with the Br atom situated above the molecular plane, that is prompt to eject Br(-). The two short-lived intermediates, which show a substantial difference in their absorption spectra, are recognized to be the two purine tautomers (i.e., iminic 7 and aminic 3 forms). The spin density distributions of the two tautomers are quite different at the O6 and N10 positions, whereas they are very similar at the N3, C5, and C8 positions. The resonance structures of the two tautomers are discussed in some detail. B1B95/6-31+G calculations show also that the tautomerization from the iminic (7) to the aminic (3) arrangement is a water-assisted process.
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152
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Heo J, Kim NJ. DFT Study on the Nucleophilic Addition Reaction of Water and Ammonia to the Thymine Radical Cation. J Phys Chem A 2007; 111:8857-63. [PMID: 17711269 DOI: 10.1021/jp0734124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nucleophilic addition reactions of water and ammonia molecules toward the C5-C6 double bond of thymine radical cations were investigated using density functional theory. We predicted that the nucleophilic addition favored the C5-site of thymine radical cations, in contrast to the previous experimental observations in bulk solution where the addition product to the C6-site was dominant. Considering the molecular orbital factors, we estimated the relative reactivity of the C5- and C6-sites of thymine radical cations for the nucleophilic addition of ammonia. We found that the C5 was more reactive than the C6 for the small-size clusters of Thy1(NH3)n+, n = 0-2, in the gas phase and even in aqueous solution, though the difference in the reactivity between the two sites became smaller as the number of ammonia molecules increased. This variation of the reactivity was attributed to the electron density redistribution within the thymine radical cations induced by the ammonia molecules as a nucleophile. We suggest that the dominance of the C6-addition product in bulk solution is mainly due to the higher stability of the C6-addition product by solvation, rather than to the higher reactivity of the C6-site for the nucleophilic addition.
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Affiliation(s)
- Jiyoung Heo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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153
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Yun BH, Lee YA, Kim SK, Kuzmin V, Kolbanovskiy A, Dedon PC, Geacintov NE, Shafirovich V. Photosensitized oxidative DNA damage: from hole injection to chemical product formation and strand cleavage. J Am Chem Soc 2007; 129:9321-32. [PMID: 17616188 PMCID: PMC2519169 DOI: 10.1021/ja066954s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxidatively generated damage to DNA induced by a pyrenyl photosensitizer residue (Py) covalently attached to a guanine base in the DNA sequence context 5'-d(CAT[G1Py]CG2TCCTAC) in aerated solutions was monitored from the initial one-electron transfer, or hole injection step, to the formation of chemical end-products monitored by HPLC, mass spectrometry, and high-resolution gel electrophoresis. Hole injection into the DNA was initiated by two-photon excitation of the Py residue with 355 nm laser pulses, thus producing the radical cation Py*+ and hydrated electrons; the latter are trapped by O2, thus forming the superoxide anion O2*-. The decay of the Py*+ radical is correlated with the appearance of the G*+/G(-H)* radical on microsecond time scales, and O2*- combines with guanine radicals at G1 to form alkali-labile 2,5-diamino-4H-imidazolone lesions (Iz1Py). Product formation in the modified strand is smaller by a factor of 2.4 in double-stranded than in single-stranded DNA. In double-stranded DNA, hot piperidine-mediated cleavage at G2 occurs only after G1Py, an efficient hole trap, is oxidized thus generating tandem lesions. An upper limit of hole hopping rates, khh < 5 x 103 s-1 from G1*+-Py to G2 can be estimated from the known rates of the combination reaction of the G(-H)* and O2*- radicals. The formation of Iz products in the unmodified complementary strand compared to the modified strand in the duplex is approximately 10 times smaller. The formation of tandem lesions is observed even at low levels of irradiation corresponding to "single-hit" conditions when less than approximately 10% of the oligonucleotide strands are damaged. A plausible mechanism for this observation is discussed.
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154
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Fukuzumi S, Miyao H, Ohkubo K, Suenobu T. Electron-transfer oxidation properties of DNA bases and DNA oligomers. J Phys Chem A 2007; 109:3285-94. [PMID: 16833661 DOI: 10.1021/jp0459763] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetics for the thermal and photoinduced electron-transfer oxidation of a series of DNA bases with various oxidants having the known one-electron reduction potentials (E(red)) in an aqueous solution at 298 K were examined, and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of DNA bases and the intrinsic barrier of the electron transfer. Although the E(ox) value of GMP at pH 7 is the lowest (1.07 V vs SCE) among the four DNA bases, the highest E(ox) value (CMP) is only 0.19 V higher than that of GMP. The selective oxidation of GMP in the thermal electron-transfer oxidation of GMP results from a significant decrease in the pH dependent oxidation potential due to the deprotonation of GMP*+. The one-electron reduced species of the photosensitizer produced by photoinduced electron transfer are observed as the transient absorption spectra when the free energy change of electron transfer is negative. The rate constants of electron-transfer oxidation of the guanine moieties in DNA oligomers with Fe(bpy)3(3+) and Ru(bpy)3(3+) were also determined using DNA oligomers containing different guanine (G) sequences from 1 to 10 G. The rate constants of electron-transfer oxidation of the guanine moieties in single- and double-stranded DNA oligomers with Fe(bpy)3(2+) and Ru(bpy)3(3+) are dependent on the number of sequential guanine molecules as well as on pH.
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Affiliation(s)
- Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, SORST, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan.
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155
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Kawai K, Osakada Y, Sugimoto A, Fujitsuka M, Majima T. Hole Transfer Rates in A-Form DNA/2′-OMeRNA Hybrid. Chemistry 2007; 13:2386-91. [PMID: 17163564 DOI: 10.1002/chem.200601210] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The hole transfer rates in the DNA/DNA B-form duplex and DNA/2'-OMeRNA A-form duplex were measured which occurred in the time range of approximately 100 micros. The hole transfer rates in the A-form duplexes were slower and more strongly dependent on the temperature compared to those in the B-form duplexes, suggesting that the A-form is more rigid than the B-form duplex in this time scale.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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156
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Manoj P, Mohan H, Mittal J, Manoj V, Aravindakumar C. Charge transfer from 2-aminopurine radical cation and radical anion to nucleobases: A pulse radiolysis study. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2006.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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157
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Adhikary A, Kumar A, Becker D, Sevilla MD. The guanine cation radical: investigation of deprotonation states by ESR and DFT. J Phys Chem B 2006; 110:24171-80. [PMID: 17125389 PMCID: PMC2526163 DOI: 10.1021/jp064361y] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work reports ESR studies that identify the favored site of deprotonation of the guanine cation radical (G*+) in an aqueous medium at 77 K. Using ESR and UV-visible spectroscopy, one-electron oxidized guanine is investigated in frozen aqueous D2O solutions of 2'-deoxyguanosine (dGuo) at low temperatures at various pHs at which the guanine cation radical, G*+ (pH 3-5), singly deprotonated species, G(-H)* (pH 7-9), and doubly deprotonated species, G(-2H)*- (pH > 11), are found. C-8-deuteration of dGuo to give 8-D-dGuo removes the major proton hyperfine coupling at C-8. This isolates the anisotropic nitrogen couplings for each of the three species and aids our analyses. These anisotropic nitrogen couplings were assigned to specific nitrogen sites by use of 15N-substituted derivatives at N1, N2, and N3 atoms in dGuo. Both ESR and UV-visible spectra are reported for each of the species: G*+, G(-H)*, and G(-2H)*-. The experimental anisotropic ESR hyperfine couplings are compared to those obtained from DFT calculations for the various tautomers of G(-H)*. Using the B3LYP/6-31G(d) method, the geometries and energies of G*+ and its singly deprotonated state in its two tautomeric forms, G(N1-H)* and G(N2-H)*, were investigated. In a nonhydrated state, G(N2-H)* is found to be more stable than G(N1-H)*, but on hydration with seven water molecules G(N1-H)* is found to be more stable than G(N2-H)*. The theoretically calculated hyperfine coupling constants (HFCCs) of G*+, G(N1-H)*, and G(-2H)*- match the experimentally observed HFCCs best on hydration with seven or more waters. For G(-2H)*-, the hyperfine coupling constant (HFCC) at the exocyclic nitrogen atom (N2) is especially sensitive to the number of hydrating water molecules; good agreement with experiment is not obtained until nine or 10 waters of hydration are included.
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Affiliation(s)
| | - Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309
| | - David Becker
- Department of Chemistry, Oakland University, Rochester, MI 48309
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158
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Abstract
Guanine bases in DNA are the most sensitive to oxidation. A lot of effort has been devoted to the understanding of the chemical modifications of guanine under different oxidizing conditions, the final goal being to know which lesions in DNA can be expected in vivo and their biological consequences. This article analyses the mechanisms underlying guanine oxidation by the comparison between one- and two-electron transfer processes. The different oxidants used in vitro give complementary answers. This overview presents a choice of some key intermediates and the predictive description of G-oxidation products that can be generated from these intermediates depending on the reaction conditions.
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Affiliation(s)
- Geneviève Pratviel
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France.
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159
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Ohkubo K, Yukimoto K, Fukuzumi S. Direct detection of nucleotide radical cations produced by electron-transfer oxidation of DNA bases with electron-transfer state of 9-mesityl-10-methylacridinium ion and resulting efficient DNA cleavage without oxygen. Chem Commun (Camb) 2006:2504-6. [PMID: 16758030 DOI: 10.1039/b601418f] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoinduced electron transfer of DNA as well as DNA bases with 9-mesityl-10-methylacridinium ion results in formation of all types of DNA base radical cations, which have been detected as the transient absorption spectra measurements, leading to efficient DNA cleavage in the absence of O2.
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Affiliation(s)
- Kei Ohkubo
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, SORST, Japan Science and Technology Agency (JST), Suita, Osaka, 565-0871, Japan
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160
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Adhikary A, Becker D, Collins S, Koppen J, Sevilla MD. C5'- and C3'-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2'-deoxyadenosine and its derivatives. Nucleic Acids Res 2006; 34:1501-11. [PMID: 16537838 PMCID: PMC1401510 DOI: 10.1093/nar/gkl026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ∼5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ∼12. 13C substitution at C5′ in dAdo yields 13C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-13C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated 13C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation.
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Affiliation(s)
| | | | | | | | - Michael D. Sevilla
- To whom correspondence should be addressed. Tel: +1 248 370 2328; Fax: +1 248 370 2321;
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161
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Evans SE, Mon S, Singh R, Ryzhkov LR, Szalai VA. DNA Oxidation in Anionic Reverse Micelles: Ruthenium-Mediated Damage at Guanine in Single- and Double-Stranded DNA. Inorg Chem 2006; 45:3124-32. [PMID: 16562969 DOI: 10.1021/ic0521022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One-electron guanine oxidation in DNA has been investigated in anionic reverse micelles (RMs). A photochemical method for generating Ru3+ from the ruthenium polypyridyl complex tris(2-2'-bipyridine)ruthenium(II) chloride ([Ru(bpy)3]Cl2) is combined with high-resolution polyacrylamide gel electrophoresis (PAGE) to quantify piperidine-labile guanine oxidation products. As characterized by emission spectroscopy of Ru(bpy)3(2+), the addition of DNA to RMs containing Ru(bpy)3(2+) does not perturb the environment of Ru(bpy)3(2+). The steady-state quenching efficiency of Ru(bpy)3(2+) with K3[Fe(CN)6] in buffer solution is approximately 2-fold higher than that observed in RMs. Consistent with the difference in quenching efficiency in the two media, a 1.5-fold higher yield of piperidine-labile damage products as monitored by PAGE is observed for duplex oligonucleotide in buffer vs RMs. In contrast, a 13-fold difference in the yield of PAGE-detected G oxidation products is observed when single-stranded DNA is the substrate. Circular dichroism spectra showed that single-stranded DNA undergoes a structural change in anionic RMs. This structural change is potentially due to cation-mediated adsorption of the DNA phosphates on the anionic headgroups of the RMs, leading to protection of the guanine from oxidatively generated damage.
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Affiliation(s)
- Sarah E Evans
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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162
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Ríos-Font R, Bertran J, Rodríguez-Santiago L, Sodupe M. Effects of Ionization, Metal Cationization and Protonation on 2‘-Deoxyguanosine: Changes on Sugar Puckering and Stability of the N-Glycosidic Bond. J Phys Chem B 2006; 110:5767-72. [PMID: 16539523 DOI: 10.1021/jp056089i] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of oxidation, protonation, and metal cationization with Cu(+) and Cu(2+) on the strength of the N-glycosidic bond in 2'-deoxyguanosine has been studied by means of quantum chemical calculations. In all cases, the N9-C1' bond distance increases (0.03-0.06 A) upon introducing positive charge in the guanine moiety, the observed variations being more important for the dicationic systems. Binding energies show that the effect of X(n)(+) in guanine hinders the homolytic dissociation, whereas it largely favors the heterolytic process. With respect to the deoxyribose ring, it has been found that metal binding, oxidation, and protonation do not significantly change the values of the phase angle of pseudorotation P. However, the glycosyl torsion angle chi varies considerably (from 242.0 degrees to 189.8 degrees) as a consequence of a stabilizing guanine-sugar (H8-O4') interaction due to the increase of acidity of guanine C8-H8 upon cationization.
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Affiliation(s)
- R Ríos-Font
- Departament de Quimica, Unitat de Quimica Fisica, Universitat Autonoma de Barcelona, Edifici Cn, 08193 Bellaterra, Barcelona, Spain
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163
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Kuimova MK, Cowan AJ, Matousek P, Parker AW, Sun XZ, Towrie M, George MW. Monitoring the direct and indirect damage of DNA bases and polynucleotides by using time-resolved infrared spectroscopy. Proc Natl Acad Sci U S A 2006; 103:2150-3. [PMID: 16467159 PMCID: PMC1413690 DOI: 10.1073/pnas.0506860103] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleotide 5'-dGMP and polynucleotide poly(dGdC).poly(dGdC) have been irradiated by using a 200-fs, 200-nm laser pulses and spectrally characterized by using time-resolved infrared spectroscopy. Under the experimental conditions, 200-nm excitation generates both electronic excited states and radical cations through photoionization; the former decay rapidly to vibrationally hot ground state. By using infrared signatures we have been able to follow these processes, and at time scales of >1 ns we observe an infrared marker band at 1,702 cm(-1) within both 5'-dGMP and the polynucleotide assigned to a photoionized product of guanine. This transient has also been reproduced through indirect chemistry through the reaction with photogenerated carbonate radical with 5'-dGMP. The ability to use time-resolved infrared spectroscopy in this way paves the way for developing solution-phase studies to investigate both direct and indirect radiation chemistry of DNA.
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Affiliation(s)
- Marina K. Kuimova
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Alexander J. Cowan
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Pavel Matousek
- Central Laser Facility, Council for the Central Laboratory of the Research Councils, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Anthony W. Parker
- Central Laser Facility, Council for the Central Laboratory of the Research Councils, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
- To whom correspondence may be addressed. E-mail:
or
| | - Xue Zhong Sun
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
| | - Michael Towrie
- Central Laser Facility, Council for the Central Laboratory of the Research Councils, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Michael W. George
- *School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom; and
- To whom correspondence may be addressed. E-mail:
or
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164
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Kawai K, Kimura T, Yoshida H, Sugimoto A, Tojo S, Fujitsuka M, Majima T. Formation of Pyrene Dimer Radical Cation at the Minor Groove of DNA. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2006. [DOI: 10.1246/bcsj.79.312] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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165
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166
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Kupan A, Saulière A, Broussy S, Seguy C, Pratviel G, Meunier B. Guanine Oxidation by Electron Transfer: One- versus Two-Electron Oxidation Mechanism. Chembiochem 2005; 7:125-33. [PMID: 16323222 DOI: 10.1002/cbic.200500284] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The degeneracy of the guanine radical cation, which is formed in DNA by oxidation of guanine by electron transfer, was studied by a detailed analysis of the oxidation products of guanine on oligonucleotide duplexes and by labeling experiments. It was shown that imidazolone, the major product of guanine oxidation, is formed through a one-electron oxidation process and incorporates one oxygen atom from O2. The formation of 8-oxo-7,8-dihydroguanine by a two-electron oxidation process was a minor pathway. The two-electron oxidation mechanism was also evidenced by the formation of a tris(hydroxymethyl)aminomethane adduct.
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Affiliation(s)
- Adam Kupan
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, 31077 Toulouse Cedex4, France
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167
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Adhikary A, Malkhasian AYS, Collins S, Koppen J, Becker D, Sevilla MD. UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures. Nucleic Acids Res 2005; 33:5553-64. [PMID: 16204456 PMCID: PMC1243799 DOI: 10.1093/nar/gki857] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
This work presents evidence that photo-excitation of guanine radical cations results in high yields of deoxyribose sugar radicals in DNA, guanine deoxyribonucleosides and deoxyribonucleotides. In dsDNA at low temperatures, formation of C1′• is observed from photo-excitation of G•+ in the 310–480 nm range with no C1′• formation observed ≥520 nm. Illumination of guanine radical cations in 2′dG, 3′-dGMP and 5′-dGMP in aqueous LiCl glasses at 143 K is found to result in remarkably high yields (∼85–95%) of sugar radicals, namely C1′•, C3′• and C5′•. The amount of each of the sugar radicals formed varies dramatically with compound structure and temperature of illumination. Radical assignments were confirmed using selective deuteration at C5′ or C3′ in 2′-dG and at C8 in all the guanine nucleosides/tides. Studies of the effect of temperature, pH, and wavelength of excitation provide important information about the mechanism of formation of these sugar radicals. Time-dependent density functional theory calculations verify that specific excited states in G•+ show considerable hole delocalization into the sugar structure, in accord with our proposed mechanism of action, namely deprotonation from the sugar moiety of the excited molecular radical cation.
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Affiliation(s)
| | | | | | | | | | - Michael D. Sevilla
- To whom correspondence should be addressed. Tel: +1 248 370 2328; Fax: +1 248 370 2321;
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168
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Solvent effect on the products of γ-irradiation of hydroxyimides and hydroxybenzotriazole. Radiat Phys Chem Oxf Engl 1993 2005. [DOI: 10.1016/j.radphyschem.2005.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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169
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Glaser R, Wu H, Lewis M. Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation. J Am Chem Soc 2005; 127:7346-58. [PMID: 15898783 DOI: 10.1021/ja0501159] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Effects are discussed of the anisotropic DNA environment on nitrosative guanine deamination based on results of an ab initio study of the aggregate 3 formed by guaninediazonium ion 1 and cytosine 2. Within 3, the protonation of 2 by 1 is fast and exothermic and forms 6, an aggregate between betaine 4 (2-diazonium-9H-purin-6-olate) and cytosinium ion 5. Electronic structure analysis of 4 shows that this betaine is not mesoionic; only the negative charge is delocalized in the pi-system while the positive charge resides in the sigma-system. Potential energy surface exploration shows that both dediazoniation and ring-opening of betaine 4 in aggregate 6 are fast and exothermic and lead irreversibly to E-11, the aggregate between (E)-5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole E-10 and 5. The computed pair binding energies for 3, 6, and E-11 greatly exceed the GC pair binding energy. While 1 can be a highly reactive intermediate in reactions of the "free nucleobase" (or its nucleoside and nucleotide), the cyanoimine 10 emerges as the key intermediate in nitrosative guanine deamination in ds-DNA and ds-oligonucleotides. In essence, the complementary nucleobase cytosine provides base catalysis and switches the sequence of deprotonation and dediazoniation. It is argued that this environment-induced switch causes entirely different reaction paths to products as compared to the respective "free nucleobase" chemistry, and the complete consistency is demonstrated of this mechanistic model with all known experimental results. Products might form directly from 10 by addition and ring closure, or their formation might involve water catalysis via 5-cyanoamino-4-imidazolecarboxylic acid 12 and/or 5-carbodiimidyl-4-imidazolecarboxylic acid 13. The pyrimidine ring-opened intermediates 10, 12, and 13 can account for the formations of xanthosine, the pH dependency and the environment dependency of oxanosine formation, the formation of the classical cross-link dG(N(2)())-to-dG(C2), including the known sequence specificity of its formation, and the formation of the structure-isomeric cross-link dG(N1)-to-dG(C2).
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Affiliation(s)
- Rainer Glaser
- Department of Chemistry, University of Missouri-Columbia, 65211, USA.
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170
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Misiaszek R, Uvaydov Y, Crean C, Geacintov NE, Shafirovich V. Combination Reactions of Superoxide with 8-Oxo-7,8-dihydroguanine Radicals in DNA. J Biol Chem 2005; 280:6293-300. [PMID: 15590679 DOI: 10.1074/jbc.m412253200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the major biomarkers of oxidative stress and oxidative damage of cellular DNA is 8-oxo-7,8-dihydroguanine (8-oxoGua), which is more easily oxidized than guanine to diverse oxidative products. In this work, we have investigated further oxidative transformations of 8-oxoGua in single- and double-stranded oligonucleotides to the dehydroguanidinohydantoin, oxaluric acid, and diastereomeric spiroiminodihydantoin lesions. The relative distributions of these end products were explored by a combined kinetic laser spectroscopy and mass spectrometry approach and are shown to depend markedly on the presence of superoxide radical anions. The 8-oxaGua radicals were produced by one-electron oxidation of 8-oxoGua by 2-aminopurine radicals generated by the two-photon ionization of 2-aminopurine residues site specifically positioned in 5'-d(CC[2-aminopurine]TC[8-oxoGua]CTACC). The hydrated electrons also formed in the photoionization process were trapped by dissolved molecular oxygen thus producing superoxide. A combination reaction between the 8-oxoGua and superoxide radicals occurs with the rate constant of (1.3 +/- 0.2) x 10(8) m(-1) s(-1) and (1.0 +/- 0.5) x 10(8) m(-1) s(-1) in single- and double-stranded DNA, respectively. The major end products of this reaction are the dehydroguanidinohydantoin lesions that slowly hydrolyze to oxaluric acid residues. In the presence of Cu,Zn-superoxide dismutase, an enzyme that induces the rapid catalytic dismutation of superoxide to the less reactive H(2)O(2) and O(2), the yields of the dehydroguanidinohydantion lesions become negligible. Under these conditions, the 8-oxoGua radicals do not exhibit any observable reactivities with oxygen (k < 10(2) m(-1) s(-1)), decay on the time interval of several seconds, and the major reaction products are the spiroiminodihydantoin lesions. The possible biological implications of the 8-oxoGua oxidation are discussed.
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Affiliation(s)
- Richard Misiaszek
- Chemistry Department and Radiation and Solid State Laboratory, New York University, New York, New York 10003-5180, USA
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171
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Heo J, Prutzman KC, Mocanu V, Campbell SL. Mechanism of free radical nitric oxide-mediated Ras guanine nucleotide dissociation. J Mol Biol 2005; 346:1423-40. [PMID: 15713491 DOI: 10.1016/j.jmb.2004.12.050] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Revised: 12/03/2004] [Accepted: 12/21/2004] [Indexed: 11/18/2022]
Abstract
Ras proteins cycle between GDP-bound and GTP-bound states to modulate a diverse array of cellular growth processes. In this study, we have elucidated a mechanism by which nitric oxide, in the presence of oxygen (NO/O2), regulates Ras activity. We show that treatment of Ras with NO/O2 causes conversion of Ras-bound GDP into a free 463.3 Da nucleotide-nitration product. Mass and UV/visible spectroscopic analyses suggest that this nitration product is 5-guanidino-4-nitroimidazole diphosphate (NIm-DP), a degradation product of 5-nitro-GDP. These results indicate that NO/O2 mediates Ras guanine nucleotide exchange (GNE) by conversion of Ras-bound GDP into an unstable 5-nitro-GDP. 5-Nitro-GDP can be produced by radical-based reaction of the GDP guanine base with nitrogen dioxide (*NO2). We also provide evidence that the Ras Phe28 side-chain plays a key role in the formation of a NO/O2-induced Ras 5-nitro-GDP product. We previously proposed a mechanism of NO/O2-mediated Ras GNE, in which *NO2, formed by the reaction of NO with O2, generates a Ras Cys118 thiyl radical (Ras-S118) intermediate. In the present study, we provide evidence for a radical-based mechanism of NO/O2-mediated Ras GNE. According to this mechanism, reaction of NO with O2 produces *NO2. *NO2 then reacts with Ras to produce Ras-S118, which withdraws an electron from the Ras-bound guanine nucleotide base to produce a guanine nucleotide diphosphate cation radical (G(+)-DP) via the Phe28 side-chain. G(+)-DP is subsequently converted to a neutral radical, and can react with another *NO2 to produce 5-nitro-GDP. This radical-based reaction process disrupts key binding interactions between Ras and the guanine base, resulting in release of GDP from Ras and its conversion to free 5-nitro-GDP. This mechanism is likely to be common to other NKCD motif-containing Ras superfamily GTPases, as NO/O2 also facilitates GNE on the redox-active Rap1A and Rab3A GTPases.
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Affiliation(s)
- Jongyun Heo
- Department of Biochemistry and Biophysics, The University of North Carolina, 530 Mary Ellen Jones Building, Chapel Hill, NC 27599-7260, USA
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172
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Ly A, Tran NQ, Sullivan K, Bandong SL, Milligan JR. Involvement of proton transfer in the reductive repair of DNA guanyl radicals by aniline derivatives. Org Biomol Chem 2005; 3:917-23. [PMID: 15731879 DOI: 10.1039/b418681h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most easily oxidized sites in DNA are the guanine bases, and major intermediates produced by the direct effect of ionizing radiation (ionization of the DNA itself) are electron deficient guanine species. By means of a radiation chemical method (gamma-irradiation of aqueous thiocyanate), we are able to produce these guanyl radicals in dilute aqueous solutions of plasmid DNA where the direct effect would otherwise be negligible. Stable modified guanine products are formed from these radicals. They can be detected in the plasmid conversion to strand breaks after a post-irradiation incubation with a DNA base excision endonuclease enzyme. If aniline compounds are also present, the yield of modified guanines is strongly attenuated. The mechanism responsible for this effect is electron donation from the aniline compound to the guanyl radical, and it is possible to derive rate constants for this reaction. Aniline compounds bearing electron withdrawing groups (e.g., 4-CF3) were found to be less reactive than those bearing electron donating groups (e.g., 4-CH3). At physiological pH values, the reduction of a guanyl radical involves the transfer of a proton as well as of an electron. The mild dependence of the rate constant on the driving force suggests that the electron is not transferred before the proton. Although the source of the proton is unclear, our observations emphasize the importance of an accompanying proton transfer in the reductive repair of oxidative damage to guanine bases which are located in a biologically active double stranded plasmid DNA substrate.
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Affiliation(s)
- Anne Ly
- Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610, USA
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173
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Shukla LI, Adhikary A, Pazdro R, Becker D, Sevilla MD. Formation of 8-oxo-7,8-dihydroguanine-radicals in gamma-irradiated DNA by multiple one-electron oxidations. Nucleic Acids Res 2004; 32:6565-74. [PMID: 15601999 PMCID: PMC545457 DOI: 10.1093/nar/gkh989] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Electron spin resonance (ESR) studies of radicals formed by radiation-induced multiple one-electron oxidations of guanine moieties in DNA are reported in this work. Annealing of gamma-irradiated DNA from 77 to 235 K results in the hydration of one electron oxidized guanine (G*+) to form the 8-hydroxy-7,8-dihydroguanin-7-yl-radical (*GOH) having one beta-proton coupling of 17-28 G and an anisotropic nitrogen coupling, A(parallel), of approximately 20 G, A(perpendicular) = 0 with g(parallel) = 2.0026 and g(perpendicular) = 2.0037. Further annealing to 258 K results in the formation of a sharp singlet at g = 2.0048 with line-width of 5.3 G that is identified as the 8-oxo-7,8-dihydroguanine one-electron-oxidized radical (8-oxo-G*+). This species is formed via two one-electron oxidations of *GOH. These two one-electron oxidation steps leading to the formation of 8-oxo-G*+ from *GOH in DNA, are in accordance with the expected ease of oxidation of *GOH and 8-oxo-G. The incorporation of oxygen from water in G*+ leading to *GOH and to 8-oxo-G*+ is verified by ESR studies employing 17O isotopically enriched water, which provide unambiguous evidence for the formation of both radicals. ESR analysis of irradiated-DNA in the presence of the electron scavenger, Tl3+, demonstrates that the cationic pathway leads to the formation of the 8-oxo-G*+. In irradiated DNA-Tl3+ samples, Tl3+ captures electrons. Tl2+ thus produced is a strong oxidant (2.2 V), which is metastable at 77 K and is observed to increase the formation of G*+ and subsequently of 8-oxo-G*+ upon annealing. We find that in the absence of the electron scavenger the yield of 8-oxo-G*+ is substantially reduced as a result of electron recombinations with G*+ and possible reaction with *GOH.
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Affiliation(s)
- Lata I Shukla
- Department of Chemistry, Oakland University, Rochester, MI 38309, USA
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174
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Sun L, Bu Y. Marked Variations of Dissociation Energy and H-Bond Character of the Guanine-Cytosine Base Pair Induced by One-Electron Oxidation and Li+ Cation Coupling. J Phys Chem B 2004; 109:593-600. [PMID: 16851051 DOI: 10.1021/jp0459817] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The variation of dissociation energy and H-bond character of the G-C cation and the Li-GC cation have been investigated by employing density functional theory (B3LYP) with the 6-31+G* basis set. The one-electron oxidation and the coupling of Li(+) to the guanine-cytosine base pair can strengthen the interaction between guanine and cytosine. The interaction of the cation Li(+) with guanine is attractive and is attributed to the polarization of the H-bonds between G-C that enhances G-C interaction. The cooperativity of the three H-bonds in the GC and Li-GC cations is different from that in the neutral GC base pair. The proton-transfer process between N(1) of the guanine and N(3) of the cytosine can occur in the GC cation and the Li-GC cation. The geometries of the transition state are out of plane, especially for the transition state of the Li-GC cation. The analysis of the activation energy for the proton-transfer process shows that the GC(+) before and after proton transfer can exist simultaneously in the gas phase, but for the Li-GC(+) system, the Li-GC(+) without proton transfer is the dominating species in the gas phase.
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Affiliation(s)
- Lixiang Sun
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China
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175
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Kawai K, Takada T, Nagai T, Cai X, Sugimoto A, Fujitsuka M, Majima T. Long-lived charge-separated state leading to DNA damage through hole transfer. J Am Chem Soc 2004; 125:16198-9. [PMID: 14692755 DOI: 10.1021/ja038309g] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hole transfer causes the long-lived charge-separated state in DNA during the photosensitized one-electron oxidation of DNA. The combination of the transient absorption measurement and DNA damage quantification by HPLC clearly demonstrated that the yield of the DNA damage correlates well with the lifetime of the charge-separated state.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan.
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176
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LeBard DN, Lilichenko M, Matyushov DV, Berlin YA, Ratner MA. Solvent Reorganization Energy of Charge Transfer in DNA Hairpins. J Phys Chem B 2003. [DOI: 10.1021/jp035546x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David N. LeBard
- Department of Chemistry and Biochemistry and the Center for the Study of Early Events in Photosynthesis, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, and Department of Chemistry and Center for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Mark Lilichenko
- Department of Chemistry and Biochemistry and the Center for the Study of Early Events in Photosynthesis, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, and Department of Chemistry and Center for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Dmitry V. Matyushov
- Department of Chemistry and Biochemistry and the Center for the Study of Early Events in Photosynthesis, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, and Department of Chemistry and Center for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Yuri A. Berlin
- Department of Chemistry and Biochemistry and the Center for the Study of Early Events in Photosynthesis, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, and Department of Chemistry and Center for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
| | - Mark A. Ratner
- Department of Chemistry and Biochemistry and the Center for the Study of Early Events in Photosynthesis, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, and Department of Chemistry and Center for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
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